The immunoglobulin superfamily (IgSF) includes immunoglobulins and numerous other cell surface and soluble molecules that mediate recognition, adhesion or binding functions in the immune system. They share partial amino acid sequence homology and tertiary structural features that were originally identified in immunoglobulin (Ig) heavy and light chains.
Molecules of the IgSF are identified by a characteristic IgSF fold structure, a sandwich structure formed by two β-sheets, packed face-to-face and linked by a disulphide bond between the B and F strands (Bork 1994; Chothia 1998). IgSF frameworks are further classified into 3-4 major categories, the Variable (V)-, Constant (C)-, I- and I2-sets, based on β-strand number, configuration and hydrogen bond patterns (Bork 1994; Cassasnovas 1998).
Conventional immunoglobulins have two heavy polypeptide chains linked by disulphide bonds at a hinge portion, and two light polypeptide chains, each of which is linked to a respective heavy chain by disulphide bonding. Each heavy chain comprises a variable (VH) domain at the N-terminal end and a number of constant (CH) domains. Each light chain has a variable (VL) domain at the N-terminal end and a constant (CL) domain at the C-terminal end, the VL and CL domains aligning with the VH domain and the first CH domain, respectively. Unlike immunoglobulins, T-cell receptors (TCRs) are heterodimers having α and β chains of equal size, each chain consisting of an N-terminal variable domain (Vα or Vβ) and a constant domain.
Typically, the variable domains on different polypeptide chains interact across hydrophobic interfaces to form binding sites designed to receive a particular target molecule. In the case of immunoglobulins, each pair of VH/VL domains form an antigen binding site, the CH and CL domains not being directly involved in binding the antibody to the antigen. Similarly, in the case of TCRs, the Vα and Vβ domains form the binding site for target molecules, namely peptides presented by a histocompatibility antigen.
The amino acid sequences of variable domains vary particularly from one molecule to another. This variation in sequence enables the molecules to recognise an extremely wide variety of target molecules. Variable domains are often viewed as comprising four framework regions, whose sequences are relatively conserved, connected by three hypervariable or complementarity determining loop regions (CDRs) (Kabat 1983 & 1987; Bork 1994). The CDRs are held in close proximity by the framework regions and, with the CDRs from the other variable domain, contribute to the formation of the binding site.
With the development of new molecular biology and recombinant DNA techniques, research interest in the IgSF field has increased. Among the main reasons for this increased interest is the desire to develop novel therapeutics and diagnostics based on immunoglobulins or other IgSF molecules.
Using the hybridoma technique developed by Kohler and Milstein, the production of monoclonal antibodies (MAbs) of almost any specificity is now well known. However, the production of human antibodies remains difficult, with the vast majority of MAbs produced being of rodent, in particular mouse, origin. Such antibodies are often antigenic in humans.
Researchers have therefore investigated producing modified immunoglobulins which are as “human” as possible, but which still retain the appropriate specificity. For example, “chimeric” antibodies have been constructed in which an animal antigen-binding variable domain is coupled to a human constant domain. The isotype of the human constant domain may be selected to tailor the chimeric antibody for participation in antibody-dependent cellular cytotoxicity (ADCC) and complement dependent cytotoxicity. However, chimeric antibodies typically may contain about one third rodent (or other non-human species) sequence and consequently are often still capable of eliciting a significant antigenic response in humans.
In a further effort to resolve the antigen binding functions of antibodies and to minimize the use of heterologous sequences in human antibodies, others have modified the specific domains by, for example, substituting rodent CDRs for CDR sequences from the corresponding segments of a human antibody. In some cases, substituting CDRs from rodent antibodies for the human CDRs in human frameworks is sufficient to transfer high antigen binding affinity as described in EP 239400.
An alternative approach has been to use fragments of immunoglobulins or other molecules of the IgSF. For example, specific binding reagents can be formed by association of only the VH and VL domains into a Fv module. Bacterial expression is then enhanced by joining the variable domains with a linker polypeptide into a single-chain scFv molecule.
Methods to improve the expression and folding characteristics of single-chain Fv molecules have been described by Nieba (1997). The properties of single V-domains, derived from natural mammalian antibodies, have been described in WO 90/05144, EP 368684 and WO 91/08482. Single camelid V-domains have been described by WO/96/34103 and in WO/94/25591. A method for reducing the hydrophobicity of the surface of a human VH domain by replacing human amino acid sequences with camelid amino acid sequences was described by Davies and Riechmann (1994). Methods to exchange other regions of human VH sequences with camel sequences to further enhance protein stability, including the insertion of cysteine residues in CDR loops, were described by Davies and Riechmann (1996).
Several attempts to engineer high-affinity single domain binding reagents using either the VH or VL domains alone have been unsuccessful, due to lack of binding specificity and the inherent insolubility of single domains exposing unpaired hydrophobic VH/VL binding faces (Kortt 1995).
The TCR has two variable domains that combine into a structure similar to the Fv module of an antibody that results from combination of the VH and VL domains. Novotny (1991) described how the Vα and Vβ domains of the TCR can be fused and expressed as a single chain polypeptide and, further, how to alter surface residues to reduce the hydrophobicity directly analogous to an antibody scFv. Other publications describe the expression characteristics of single-chain TCRs comprising two Vα and Vβ domains (Wulfing 1994; Ward 1991).
The three-dimensional crystal structures have been published for intact immunoglobulins, a variety of immunoglobulin fragments, antibody-antigen complexes and for other IgSF molecules such as the TCR. It is known that the function of IgSF molecules is dependent on their three dimensional structure, and that amino acid substitutions can change the three-dimensional structure of, for example, an antibody (Snow and Amzel 1986). Based upon molecular modelling, it has been shown that the antigen binding affinity of a humanized antibody can be increased by mutagenesis (Riechmann 1988; Queen 1989).
The Immunoglobulin New Antigen Receptors (IgNARs) are an unconventional subset of antibodies recently identified in fish. In domain structure, IgNAR proteins are reportedly similar to other immune effector molecules, being disulphide-bonded homodimers of two polypeptide chains having five constant domains (CNARs) and one variable domain (VNAR) (Greenberg 1995). However, unlike conventional antibodies, there are no associated light chains and the individual variable domains are independent in solution and do not appear to associate across a hydrophobic interface (as seen for conventional VH/VL type antibodies) (Roux 1998).
IgNARs have been identified in all shark species studied to date. In particular, IgNARs have been identified in the serum of nurse sharks Ginglymostoma cirratum (Greenberg 1995) and wobbegong sharks Orectolobus maculatus (Nuttall 2001). The cell-surface expression of IgNARs has also been reported (Rumfelt 2002). Research has implicated IgNARs as true molecules of the immune armoury, and as the most probable agents of the shark antigen-driven affinity-maturation antibody response (Diaz 1999; Nuttall 2002; Dooley 2003).
IgNARs identified to date have been placed into three categories based on their time of appearance during the shark development and on their postulated disulphide bonding pattern within the variable domains (Diaz 2002; Nuttall 2003). Type 1 VNAR topology is characterised by an extra framework disulphide linkage and, usually, cysteines in the extended loop region analogous to a conventional CDR3 loop, which it has been suggested may form intra-loop disulphide bonds. Type 2 VNAR topology is characterised by cysteines in the loop regions analogous to conventional CDR1 and CDR3 loops in approximately two thirds of cases, which it has been postulated may form inter-loop disulphide bonds. Type 3 VNAR topology is characterised by a relatively constant sized loop region analogous to a conventional CDR3 loop of limited diversity and a characteristic conserved tryptophan residue within the loop region analogous to a CDR1 loop.
Regardless of type, all IgNARs identified to date are reported as having minimally variable loop regions analogous to conventional CDR1 and CDR2 loops, with diversity being concentrated in an elongated loop region analogous to a conventional CDR3 loop (Greenberg 1995; Nuttall 2001; Diaz 2002). The elongated loop region can reportedly vary in length from 5 to 23 residues in length, though the modal classes are more in the order of 15 to 17 residues (Nuttall 2003). This is significantly larger than for conventional murine and human antibodies, but approximate to the extended CDR3 loops found in camelid single VH antibodies (Wu 1993; Muyldermans 1994).
Large bacteriophage libraries have been generated based upon the Type 2 VNAR repertoire from wobbegong sharks and used to isolate a number of Type 2 VNARs proteins encapsulating significant variability within the framework and the loop region analogous to a conventional CDR1 loop. However, the most significant diversity was within the extended loop region analogous to a conventional CDR3 loop, the extended loop region varying in both length and amino acid composition (Nuttall 2001; Nuttall 2003).
Various computer-modelled structures for Type 2 VNARs have been reported in the literature (Roux 1998; Nuttall 2001; Diaz 2002; Nuttall 2004). Although such computer modelling can offer key insights into structure, the definitive structure remains to be determined from crystallographic analysis. In the case of VNARs, the elucidation of the crystal structure is particularly important.